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Ekins M, Erpenbeck D, Wrheide G, Hooper JNA. Deep Water Polymastiidae (Porifera, Polymastiida) from the South West Pacific. Zootaxa 2023; 5369:57-88. [PMID: 38220726 DOI: 10.11646/zootaxa.5369.1.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Indexed: 01/16/2024]
Abstract
This study reports on some deep water sponges in the family Polymastiidae collected during the 2017 Abyss Cruise off the East Coast of Australia and the 2003 NORFANZ Expedition to the Lord Howe and Norfolk Ridges in the Tasman Sea, Southwest Pacific Ocean. Species of Radiella, Spinularia, Ridleia, Tentorium and Polymastia were collected from abyssal and bathyal depths. From these collections, seven new species were discovered: Radiella nidula sp. nov., Radiella pumix sp. nov., Radiella sclera sp. nov., Spinularia flagellata sp. nov., Tentorium labium sp. nov., Ridleia echidna sp. nov. and Polymastia norfanzii sp. nov. In addition, two species previously known are redescribed based on the new collections: viz. Polymastia zitteli and Polymastia invaginata.
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Affiliation(s)
- Merrick Ekins
- Queensland Museum; PO Box 3300; South Brisbane 4101; Brisbane; Queensland; Australia; School of Biological Sciences; University of Queensland; St Lucia; Queensland; 4072 Australia; Griffith Institute for Drug Discovery; Griffith University; Brisbane 4111; Queensland; Australia.
| | - Dirk Erpenbeck
- GeoBio-Center; Ludwig-Maximilians-Universitt Mnchen; Richard-Wagner-Strae 10; 80333 Munich; Germany; Dept. of Earth and Environmental Sciences Ludwig-Maximilians-Universitt Mnchen; Richard-Wagner-Strae 10; 80333 Munich; Germany SNSB Bayerische Staatssammlung fr Palontologie und Geologie; Richard-Wagner-Str. 10; 80333 Mnchen; Germany.
| | - Gert Wrheide
- GeoBio-Center; Ludwig-Maximilians-Universitt Mnchen; Richard-Wagner-Strae 10; 80333 Munich; Germany; Dept. of Earth and Environmental Sciences Ludwig-Maximilians-Universitt Mnchen; Richard-Wagner-Strae 10; 80333 Munich; Germany; SNSB Bayerische Staatssammlung fr Palontologie und Geologie; Richard-Wagner-Str. 10; 80333 Mnchen; Germany.
| | - John N A Hooper
- Queensland Museum; PO Box 3300; South Brisbane 4101; Brisbane; Queensland; Australia; Griffith Institute for Drug Discovery; Griffith University; Brisbane 4111; Queensland; Australia.
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Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates. Mar Drugs 2023; 21:md21030165. [PMID: 36976214 PMCID: PMC10054348 DOI: 10.3390/md21030165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Marine invertebrate microbiomes have been a rich source of bioactive compounds and interesting genomic features. In cases where the achievable amounts of metagenomic DNA are too low for direct sequencing, multiple displacement amplification (MDA) can be used for whole genome amplification. However, MDA has known limitations which can affect the quality of the resulting genomes and metagenomes. In this study, we evaluated the conservation of biosynthetic gene clusters (BGCs) and enzymes in MDA products from low numbers of prokaryotic cells (estimated 2–850). Marine invertebrate microbiomes collected from Arctic and sub-Arctic areas served as source material. The cells were separated from the host tissue, lysed, and directly subjected to MDA. The MDA products were sequenced by Illumina sequencing. Corresponding numbers of bacteria from a set of three reference strains were treated the same way. The study demonstrated that useful information on taxonomic, BGC, and enzyme diversities was obtainable from such marginal quantities of metagenomic material. Although high levels of assembly fragmentation resulted in most BGCs being incomplete, we conclude that this genome mining approach has the potential to reveal interesting BGCs and genes from hard-to-reach biological sources.
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Sokolova AM, Aksenova OV, Bespalaya YV, Gofarov MY, Kondakov AV, Konopleva ES, Tomilova AA, Travina OV, Tanmuangpak K, Tumpeesuwan S, Vikhrev IV, Bolotov IN. Integrative taxonomy and biogeographic affinities of the first freshwater sponge and mollusc association discovered in tropical Asia. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Agniya M. Sokolova
- N. K. Koltzov Institute of Developmental Biology of the Russian Academy of Sciences Moscow Russia
| | - Olga V. Aksenova
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
- Northern Arctic Federal University Arkhangelsk Russia
| | - Yulia V. Bespalaya
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
- Northern Arctic Federal University Arkhangelsk Russia
| | - Mikhail Y. Gofarov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
- Northern Arctic Federal University Arkhangelsk Russia
| | - Alexander V. Kondakov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
- Northern Arctic Federal University Arkhangelsk Russia
| | - Ekaterina S. Konopleva
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
- Northern Arctic Federal University Arkhangelsk Russia
| | - Alena A. Tomilova
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
| | - Oksana V. Travina
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
| | - Kitti Tanmuangpak
- Department of Science Faculty of Science and Technology Loei Rajabhat University Loei Thailand
| | - Sakboworn Tumpeesuwan
- Department of Biology Faculty of Science Mahasarakham University Maha Sarakham Thailand
| | - Ilya V. Vikhrev
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
- Northern Arctic Federal University Arkhangelsk Russia
| | - Ivan N. Bolotov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
- Northern Arctic Federal University Arkhangelsk Russia
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Georgieva MN, Taboada S, Riesgo A, Díez-Vives C, De Leo FC, Jeffreys RM, Copley JT, Little CTS, Ríos P, Cristobo J, Hestetun JT, Glover AG. Evidence of Vent-Adaptation in Sponges Living at the Periphery of Hydrothermal Vent Environments: Ecological and Evolutionary Implications. Front Microbiol 2020; 11:1636. [PMID: 32793148 PMCID: PMC7393317 DOI: 10.3389/fmicb.2020.01636] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/23/2020] [Indexed: 01/04/2023] Open
Abstract
The peripheral areas of deep-sea hydrothermal vents are often inhabited by an assemblage of animals distinct to those living close to vent chimneys. For many such taxa, it is considered that peak abundances in the vent periphery relate to the availability of hard substrate as well as the increased concentrations of organic matter generated at vents, compared to background areas. However, the peripheries of vents are less well-studied than the assemblages of vent-endemic taxa, and the mechanisms through which peripheral fauna may benefit from vent environments are generally unknown. Understanding this is crucial for evaluating the sphere of influence of hydrothermal vents and managing the impacts of future human activity within these environments, as well as offering insights into the processes of metazoan adaptation to vents. In this study, we explored the evolutionary histories, microbiomes and nutritional sources of two distantly-related sponge types living at the periphery of active hydrothermal vents in two different geological settings (Cladorhiza from the E2 vent site on the East Scotia Ridge, Southern Ocean, and Spinularia from the Endeavour vent site on the Juan de Fuca Ridge, North-East Pacific) to examine their relationship to nearby venting. Our results uncovered a close sister relationship between the majority of our E2 Cladorhiza specimens and the species Cladorhiza methanophila, known to harbor and obtain nutrition from methanotrophic symbionts at cold seeps. Our microbiome analyses demonstrated that both E2 Cladorhiza and Endeavour Spinularia sp. are associated with putative chemosynthetic Gammaproteobacteria, including Thioglobaceae (present in both sponge types) and Methylomonaceae (present in Spinularia sp.). These bacteria are closely related to chemoautotrophic symbionts of bathymodiolin mussels. Both vent-peripheral sponges demonstrate carbon and nitrogen isotopic signatures consistent with contributions to nutrition from chemosynthesis. This study expands the number of known associations between metazoans and potentially chemosynthetic Gammaproteobacteria, indicating that they can be incredibly widespread and also occur away from the immediate vicinity of chemosynthetic environments in the vent-periphery, where these sponges may be adapted to benefit from dispersed vent fluids.
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Affiliation(s)
| | - Sergi Taboada
- Life Sciences Department, Natural History Museum, London, United Kingdom
- Departamento de Biología (Zoología), Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Zoología y Antropología Física, Universidad de Alcalá, Madrid, Spain
| | - Ana Riesgo
- Life Sciences Department, Natural History Museum, London, United Kingdom
| | | | - Fabio C. De Leo
- Ocean Networks Canada, University of Victoria, Victoria, BC, Canada
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Rachel M. Jeffreys
- School of Environmental Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jonathan T. Copley
- School of Ocean and Earth Science, University of Southampton, Southampton, United Kingdom
| | - Crispin T. S. Little
- Life Sciences Department, Natural History Museum, London, United Kingdom
- School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Pilar Ríos
- Departamento de Zoología y Antropología Física, Universidad de Alcalá, Madrid, Spain
- Centro Oceanográfico de Santander, Instituto Español de Oceanografía, Santander, Spain
| | - Javier Cristobo
- Departamento de Zoología y Antropología Física, Universidad de Alcalá, Madrid, Spain
- Centro Oceanográfico de Gijón, Instituto Español de Oceanografía, Gijón, Spain
| | - Jon T. Hestetun
- NORCE Environment, Norwegian Research Centre (NORCE), Bergen, Norway
| | - Adrian G. Glover
- Life Sciences Department, Natural History Museum, London, United Kingdom
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Shaffer MR, Davy SK, Bell JJ. Hidden diversity in the genus Tethya: comparing molecular and morphological techniques for species identification. Heredity (Edinb) 2018; 122:354-369. [PMID: 30131516 DOI: 10.1038/s41437-018-0134-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/25/2018] [Accepted: 07/29/2018] [Indexed: 11/09/2022] Open
Abstract
Correctly determining species' identity is critical for estimating biodiversity and effectively managing marine populations, but is difficult for species that have few morphological traits or are highly plastic. Sponges are considered a taxonomically difficult group because they lack multiple consistent diagnostic features, which coupled with their common phenotypic plasticity, makes the presence of species complexes likely, but difficult to detect. Here, we investigated the evolutionary relationship of Tethya spp. in central New Zealand using both molecular and morphological techniques to highlight the potential for cryptic speciation in sponges. Phylogenetic reconstructions based on two mitochondrial markers (rnl, COI-ext) and one nuclear marker (18S) revealed three genetic clades, with one clade representing Tethya bergquistae and two clades belonging to what was a priori thought to be a single species, Tethya burtoni. Eleven microsatellite markers were also used to further resolve the T. burtoni group, revealing a division consistent with the 18S and rnl data. Morphological analysis based on spicule characteristics allowed T. bergquistae to be distinguished from T. burtoni, but revealed no apparent differences between the T. burtoni clades. Here, we highlight hidden genetic diversity within T. burtoni, likely representing a group consisting of incipient species that have undergone speciation but have yet to express clear morphological differences. Our study supports the notion that cryptic speciation in sponges may go undetected and diversity underestimated when using only morphology-based taxonomy, which has broad scale implications for conservation and management of marine systems.
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Affiliation(s)
- Megan R Shaffer
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand.
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand
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Alvizu A, Eilertsen MH, Xavier JR, Rapp HT. Increased taxon sampling provides new insights into the phylogeny and evolution of the subclass Calcaronea (Porifera, Calcarea). ORG DIVERS EVOL 2018. [DOI: 10.1007/s13127-018-0368-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Morozov G, Sabirov RM, Anisimova N. New data on sponges from Svalbard Archipelago with a description of a new species of Halicnemia. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1440020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Grigori Morozov
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russia
| | - Rushan Mirzovich Sabirov
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russia
| | - Natalia Anisimova
- Laboratory of Trophology, Knipovich Polar Research Institute of Marine Fisheries and Oceanography, Murmansk, Russia
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Yang Q, Franco CMM, Sorokin SJ, Zhang W. Development of a multilocus-based approach for sponge (phylum Porifera) identification: refinement and limitations. Sci Rep 2017; 7:41422. [PMID: 28150727 PMCID: PMC5288722 DOI: 10.1038/srep41422] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/19/2016] [Indexed: 01/29/2023] Open
Abstract
For sponges (phylum Porifera), there is no reliable molecular protocol available for species identification. To address this gap, we developed a multilocus-based Sponge Identification Protocol (SIP) validated by a sample of 37 sponge species belonging to 10 orders from South Australia. The universal barcode COI mtDNA, 28S rRNA gene (D3-D5), and the nuclear ITS1-5.8S-ITS2 region were evaluated for their suitability and capacity for sponge identification. The highest Bit Score was applied to infer the identity. The reliability of SIP was validated by phylogenetic analysis. The 28S rRNA gene and COI mtDNA performed better than the ITS region in classifying sponges at various taxonomic levels. A major limitation is that the databases are not well populated and possess low diversity, making it difficult to conduct the molecular identification protocol. The identification is also impacted by the accuracy of the morphological classification of the sponges whose sequences have been submitted to the database. Re-examination of the morphological identification further demonstrated and improved the reliability of sponge identification by SIP. Integrated with morphological identification, the multilocus-based SIP offers an improved protocol for more reliable and effective sponge identification, by coupling the accuracy of different DNA markers.
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Affiliation(s)
- Qi Yang
- Centre for Marine Bioproducts Development, Flinders University, Adelaide, South Australia, SA 5042, Australia.,Department of Medical Biotechnology, School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, South Australia, SA 5042, Australia
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, Flinders University, Adelaide, South Australia, SA 5042, Australia.,Department of Medical Biotechnology, School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, South Australia, SA 5042, Australia
| | - Shirley J Sorokin
- Centre for Marine Bioproducts Development, Flinders University, Adelaide, South Australia, SA 5042, Australia.,Department of Medical Biotechnology, School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, South Australia, SA 5042, Australia.,SARDI Aquatic Sciences, 2 Hamra Ave, West Beach, SA 5024, Australia
| | - Wei Zhang
- Centre for Marine Bioproducts Development, Flinders University, Adelaide, South Australia, SA 5042, Australia.,Department of Medical Biotechnology, School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, South Australia, SA 5042, Australia.,Centre for Marine Drugs, Renji Hospital, Shanghai Jiaotong University, Shanghai, 200240, China
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